Methods for detecting conformational changes in bioentities

1. A method for identifying the ability of a binding molecule to inhibit or enhance protein degradation, comprising:

a. immobilizing the protein on each of a separated first surface and second surface of a biosensor that can detect a change in the surface refractive index;

b. binding a binding molecule to the protein immobilized on the first surface of the biosensor but not to the protein immobilized on the second surface of the biosensor;

c. exposing the immobilized protein to one or more degrading agents such that the immobilized protein on the first surface and second surface of the biosensor reacts with the degrading agent;

d. measuring the first surface refractive index of the immobilized protein on the first surface and the second surface refractive index of the immobilized protein on the second surface of the biosensor; and

e. comparing the first surface refractive index and the second surface refractive index, wherein (1) when the second surface refractive index is less than the first surface refractive index, the binding molecule inhibits degradation of the protein, and (2) when the second surface refractive index is greater than the first surface refractive index, the binding molecule enhances degradation of the protein.

2. The method of claim 1 , wherein the binding molecule is a small molecule selected from the group consisting of a pharmaceutical drug, a metabolite, a supramolecular assembly, a nanoparticle, a polymer, and a bioentity having a molecular weight less than 300 Da.

3. The method of claim 1 , wherein the biosensor comprises a glass substrate with a layer of gold deposited on the surface of the substrate, a hafnium oxide-coated glass surface, a grating-coupled biosensor, a Fabry Perot cavity sensor, a zero-mode waveguide, a fluorescent enhanced SPR sensor, a cantilever biosensor, an impedance-based electrode detection, or a high Q whispering mode gallery cavity resonator.

4. The method of claim 1 , wherein the degrading agent comprises a protease.

5. The method of claim 4 , wherein the protease comprises a natural or synthetic protease, an extracellular protease, a metalloproteinase, or a mixture thereof.

6. The method of claim 1 , wherein the degrading agent comprises a degrading catalyst.

7. The method of claim 1 , further comprising monitoring the exposing step (c), monitoring the resultant products produced during step (c), or both by multi-mode detection.

8. The method of claim 1 , wherein in step (c), the immobilized protein is exposed to a selected degrading agent having a known concentration.